The second season of Digimon begins three years after the end of the second movie. Most of the original Chosen have moved on in life, but still keep the memories of the last summer in their hearts. Taichi and Yamato are in middle school now, as well as Koushiro and Sora. Jyou is writing his high school entrance exams, and Mimi's moved to America. Still, Takeru and Hikari continue their lives, and meet some new friends at school.

These new friends are dragged into something beyond their understanding as the original Destined recieve a distress call from the digital world about a new enemy: a human boy who is wreaking havok in the Digital World, calling himself the Digimon Kaizer. He's devised a method of controlling Digimon's minds, and has also set up a system of Black Spires, which prevent Digimon from Evolving.

Daisuke, Miyako, and Iori soon find that they, too, are DigiDestined, with their own Digimon partners and D3 devices, that allow their partners to evolve even within the influence of the black spires. After Hikari and Takeru find their D3's, they form a great team, and set out to rid the Digital World of the Digimon Kaizer's rule.